bcftools norm -m -any And check for duplicate CHROM, POS, REF, ALT I will try this and report back Author eturro commented Dec 2, 2014 Even with the above attempted workaround, I still get duplicate records. Here is a quasi-minimal example: $ bcftools view -H file1.vcf.gz 1 13946...
bcftools norm: atomization now supportsNumber=A,Rstring annotations (#1503) assign as many alternate alleles to genotypes at multiallelic sites in the-m +mode, disregarding the phase. Previously the program assumed to be executed as an inverse operation of-m -, but when that was not the case...
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vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(htslib_khash_str2int_h) $(bcftools_h) rbuf.h vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_khash_str2int_h) $(htslib_vcfutils_h) $(bcftools_h) $(...
som_norm_counts(args->som[i]); if ( args->prefix ) { char *bname = msprintf("%s.som.%d", args->prefix,i); som_create_plot(args->som[i], bname); free(bname); } }// evaluate float *good = (float*) malloc(sizeof(float)*ngood); assert(good); ...
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vcfnorm.c.pysam.c vcfplugin.c vcfplugin.c.pysam.c vcfquery.c vcfquery.c.pysam.c vcfroh.c vcfroh.c.pysam.c vcfsom.c vcfsom.c.pysam.c vcfsort.c vcfsort.c.pysam.c vcfstats.c vcfstats.c.pysam.c vcfview.c vcfview.c.pysam.c vcmp.c vcmp.c.pysam.c vcmp.h version.c ve...
vcfnorm.c.pysam.c vcfplugin.c vcfplugin.c.pysam.c vcfquery.c vcfquery.c.pysam.c vcfroh.c vcfroh.c.pysam.c vcfsom.c vcfsom.c.pysam.c vcfsort.c vcfsort.c.pysam.c vcfstats.c vcfstats.c.pysam.c vcfview.c vcfview.c.pysam.c vcmp.c vcmp.c.pysam.c vcmp.h version.c ver...
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For "vertical" merge take a look at *<<concat,bcftools concat>>* or *<<norm,bcftools norm>> -m* instead. *--force-no-index*:: synonymous to *--no-index* *--force-samples*:: if the merged files contain duplicate samples names, proceed anyway. Duplicate sample names will be ...